R markdown creates interactive reports from R code. This post provides a few tips to improve the appearance of output documents. In any case, the bible is the Rstudio documentation.
R markdown allows to easily format your text. You can add links, write in bold or italic. This is very well explained in the Rstudio cheatsheet.
Here is the code I used to make this paragraph:
R markdown allows to easily format your text. You can add [links](www.r-graph-gallery.com), write in **bold** or *italic*. This is very well explained in the [Rstudio cheatsheet](https://www.rstudio.com/wp-content/uploads/2015/02/rmarkdown-cheatsheet.pdf).
Add an horizontal line by adding 3 stars:
***
Header of level 1, 2, 3 are set using #, ## and ###. You can auto number your chapters using this option the header:
---
title: "Your title"
output:
html_document:
number_sections: TRUE
---
# Title
## A subtitle
## Another subtitle
# Another title
I really like to add spaces in my document to give it a more uncluttered look. This is done using the <br> command. This .rmd code:
A first sentence
<br><br><br><br>
A seconde sentence
will give this htmloutput
A first sentence
A seconde sentence
To center an image, use this code:
<center>

</center>
Here is the result
I find it pleasant to have a bit of space before starting a new chapter. You can use a <br> before each header. A more convenient way is to add some margin in your CSS. Create a style.css file:
h1, .h1, h2, .h2, h3, .h3 {
margin-top: 84px;
}
A rmd document that takes into account this .css file:
---
title: "A document with a CSS included"
output:
html_document:
css: style.css
---
A title will follow, but with a lot of space before it
# Title 1
content of part 1
# Title 2
content of part 2
The document you are reading uses this css. See the separation between chapters.
Specify the caption of your figure in the chunk header. Example:
{r, fig.align="center", fig.width=6, fig.height=6, fig.cap="Figure: Here is a really important caption."}
library(tidyverse)
mpg %>%
ggplot( aes(x=reorder(class, hwy), y=hwy, fill=class)) +
geom_boxplot() +
xlab("class") +
theme(legend.position="none")
Figure: Here is a really important caption.
Change the black default caption using CSS. Adding this code in your style.css file.
<style>
p.caption {
font-size: 0.9em;
font-style: italic;
color: grey;
margin-right: 10%;
margin-left: 10%;
text-align: justify;
}
</style>
file will give this result:
Figure: Here is a really important caption, customized to be grey and in italic.
The DT library is my favourite option to display tables in your document. It allows to:
library(DT)
datatable(mtcars, rownames = FALSE, filter="top", options = list(pageLength = 5, scrollX=T) )
If you share your code with somebody who’s more focus on results than code, or if your code chunks are very long, you probably want to hide the code, but still allow the reader to consult it if necessary. This is possible by modifying the YAML header of your document:
output:
html_document:
code_folding: "hide"
You can apply some css to a specific part of your document. Here is an example where I change the background color of a small part. Handy to highlight conclusions at the end of your document.
Code:
<style>
div.blue { background-color:#e6f0ff; border-radius: 5px; padding: 20px;}
</style>
<div class = "blue">
- This is my first conclusion
- This is my second conclusion
</div>
Will give: Possible to cache code. But better to use it with care. Personnaly use it at the end, just to make the document pretty.
Several solutions exist. I used the code provided in this repo. Made by Tim Holman. Just paste the provided code in your header.html, like you have done for the footer.
R allows to build any type of interactive graphic. My favourite library is plotly that will turn any of your ggplot2 graphic interactive in one supplementary line of code. Try to hover points, to select a zone, to click on the legend.
library(ggplot2)
library(plotly)
library(gapminder)
p <- gapminder %>%
filter(year==1977) %>%
ggplot( aes(gdpPercap, lifeExp, size = pop, color=continent)) +
geom_point() +
scale_x_log10() +
theme_bw()
ggplotly(p)
Customize the document appearance using one of the existing template:
Explanation in the R Markdown Websites section of the R Markdown website. To run a basic example:
library(rmarkdown)
rmarkdown::render_site()
_site folder that contains an index.html file. Open it, it is your website.If you often use the same kind of customization you probably want to create your own .rmd template. A good starting point is the Rstudio documentation.
This document is produced using my personal template: epuRate. An easy solution to create your template can be to fork / download this repo and apply your own style instead of mine.
It is a good practice to add a session info at the end of your document. It will increase reproducibility and costs only one line of code
sessionInfo()
## R version 3.4.1 (2017-06-30)
## Platform: x86_64-apple-darwin15.6.0 (64-bit)
## Running under: macOS Sierra 10.12.6
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] bindrcpp_0.2 gapminder_0.3.0 plotly_4.7.1 DT_0.2
## [5] forcats_0.2.0 stringr_1.2.0 dplyr_0.7.4 purrr_0.2.4
## [9] readr_1.1.1 tidyr_0.7.2 tibble_1.4.2 ggplot2_2.2.1
## [13] tidyverse_1.2.1 rmarkdown_1.8 epuRate_0.1
##
## loaded via a namespace (and not attached):
## [1] reshape2_1.4.3 haven_1.1.0 lattice_0.20-35
## [4] colorspace_1.3-2 viridisLite_0.2.0 htmltools_0.3.6
## [7] yaml_2.1.16 rlang_0.1.6.9003 pillar_1.1.0
## [10] foreign_0.8-69 glue_1.2.0 modelr_0.1.1
## [13] readxl_1.0.0 bindr_0.1 plyr_1.8.4
## [16] munsell_0.4.3 gtable_0.2.0 cellranger_1.1.0
## [19] rvest_0.3.2 htmlwidgets_1.1 psych_1.7.8
## [22] evaluate_0.10.1 labeling_0.3 knitr_1.18.7
## [25] httpuv_1.3.5 crosstalk_1.0.0 parallel_3.4.1
## [28] highr_0.6 broom_0.4.2 Rcpp_0.12.14
## [31] xtable_1.8-2 scales_0.5.0.9000 backports_1.1.1
## [34] jsonlite_1.5 mime_0.5 mnormt_1.5-5
## [37] hms_0.3 digest_0.6.14 stringi_1.1.5
## [40] shiny_1.0.5 grid_3.4.1 rprojroot_1.2
## [43] cli_1.0.0 tools_3.4.1 magrittr_1.5
## [46] lazyeval_0.2.1 crayon_1.3.4 pkgconfig_2.0.1
## [49] data.table_1.10.4-3 xml2_1.1.1 lubridate_1.7.1
## [52] assertthat_0.2.0 httr_1.3.1 rstudioapi_0.7
## [55] R6_2.2.2 nlme_3.1-131 compiler_3.4.1
A work by Yan Holtz
Yan.holtz.data@gmail.com